In [4]:
suppressMessages(library(ArchR))
library(parallel)
ss <- function(x, pattern, slot = 1, ...) { sapply(strsplit(x = x, split = pattern, ...), '[', slot) }
options(stringsAsFactors = F)
options(repr.plot.width=18, repr.plot.height=13)
suppressMessages(library(Seurat))
suppressMessages(library(SingleCellExperiment))
library(tidyverse)
In [6]:
##################################
### set Arrow File parameters ####
addArchRThreads(threads = 8)

##################################
### load mm ArchR genome ###
addArchRGenome('mm10')

Input threads is equal to or greater than ncores minus 1 (7)
Setting cores to ncores minus 2. Set force = TRUE to set above this number!

Setting default number of Parallel threads to 6.

Setting default genome to Mm10.
In [7]:
PROJDIR='../../../data/tidy_data/ArchRProjects'
proj = loadArchRProject(file.path(PROJDIR,'Mouse_DorsalHorn_scATAC'), showLogo = FALSE)
projNeuron = loadArchRProject(file.path(PROJDIR,'Mouse_scATAC_DorsalHorn_neuron2'), showLogo = FALSE) #neuron2 is correct proj
projGlia = loadArchRProject(file.path(PROJDIR,'Mouse_scATAC_DorsalHorn_glia'), showLogo = FALSE)

Successfully loaded ArchRProject!

Successfully loaded ArchRProject!

Successfully loaded ArchRProject!
In [8]:
proj
projNeuron
projGlia

           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    


class: ArchRProject 
outputDirectory: /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchRProjects/Mouse_DorsalHorn_scATAC 
samples(12): Mouse_DH_SEA2253A58 Mouse_DH_SEA2253A59 ...
  Mouse_DH_SEA2253A68 Mouse_DH_SEA2253A69
sampleColData names(8): ArrowFiles Sample_ID ... Species Region
cellColData names(31): Sample TSSEnrichment ... predictedGroup_RNA2ATAC
  FINAL_GROUP_LABEL
numberOfCells(1): 75955
medianTSS(1): 23.946
medianFrags(1): 16376
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    


class: ArchRProject 
outputDirectory: /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchRProjects/Mouse_scATAC_DorsalHorn_neuron2 
samples(12): Mouse_DH_SEA2253A60 Mouse_DH_SEA2253A61 ...
  Mouse_DH_SEA2253A69 Mouse_DH_SEA2253A68
sampleColData names(8): ArrowFiles Sample_ID ... Species Region
cellColData names(40): Sample TSSEnrichment ...
  predictedScore_RNA2ATAC_clustertype FINAL_GROUP_LABEL
numberOfCells(1): 20591
medianTSS(1): 20.626
medianFrags(1): 25740
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    


class: ArchRProject 
outputDirectory: /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchRProjects/Mouse_scATAC_DorsalHorn_glia 
samples(12): Mouse_DH_SEA2253A61 Mouse_DH_SEA2253A60 ...
  Mouse_DH_SEA2253A68 Mouse_DH_SEA2253A64
sampleColData names(8): ArrowFiles Sample_ID ... Species Region
cellColData names(38): Sample TSSEnrichment ... Clusters_RNALabels
  FINAL_GROUP_LABEL
numberOfCells(1): 55364
medianTSS(1): 25.181
medianFrags(1): 14350
In [5]:
#we need to standardize the column names, and choose the ones we want to keep
(names(getCellColData(projNeuron)))
(names(getCellColData(projGlia)))
  1. 'Sample'
  2. 'TSSEnrichment'
  3. 'ReadsInTSS'
  4. 'ReadsInPromoter'
  5. 'ReadsInBlacklist'
  6. 'PromoterRatio'
  7. 'PassQC'
  8. 'NucleosomeRatio'
  9. 'nMultiFrags'
  10. 'nMonoFrags'
  11. 'nFrags'
  12. 'nDiFrags'
  13. 'DoubletScore'
  14. 'DoubletEnrichment'
  15. 'BlacklistRatio'
  16. 'Sample_ID'
  17. 'Date.nuclei.prep'
  18. 'Biological.rep'
  19. 'Age'
  20. 'Sex'
  21. 'Species'
  22. 'Region'
  23. 'ClustersI200'
  24. 'ClustersH200'
  25. 'logNFrags'
  26. 'Celltype1'
  27. 'ClustersX60'
  28. 'predictedCell_Co'
  29. 'predictedGroup_RNA2ATACCo'
  30. 'predictedScore_RNA2ATACCo'
  31. 'ClustersX20'
  32. 'ClustersX10'
  33. 'predictedCell_Co_cell'
  34. 'predictedGroup_RNA2ATACCo_cell'
  35. 'predictedScore_RNA2ATACCo_cell'
  36. 'Neuron_Type'
  37. 'predictedCell_clustertype'
  38. 'predictedGroup_RNA2ATAC_clustertype'
  39. 'predictedScore_RNA2ATAC_clustertype'
  1. 'Sample'
  2. 'TSSEnrichment'
  3. 'ReadsInTSS'
  4. 'ReadsInPromoter'
  5. 'ReadsInBlacklist'
  6. 'PromoterRatio'
  7. 'PassQC'
  8. 'NucleosomeRatio'
  9. 'nMultiFrags'
  10. 'nMonoFrags'
  11. 'nFrags'
  12. 'nDiFrags'
  13. 'DoubletScore'
  14. 'DoubletEnrichment'
  15. 'BlacklistRatio'
  16. 'Sample_ID'
  17. 'Date.nuclei.prep'
  18. 'Biological.rep'
  19. 'Age'
  20. 'Sex'
  21. 'Species'
  22. 'Region'
  23. 'ClustersI200'
  24. 'ClustersH200'
  25. 'logNFrags'
  26. 'Celltype1'
  27. 'ClustersX60'
  28. 'predictedCell_Co'
  29. 'predictedGroup_RNA2ATACCo'
  30. 'predictedScore_RNA2ATACCo'
  31. 'ClustersX10_tmp'
  32. 'ClustersX10'
  33. 'ClustersX20'
  34. 'ClustersX30'
  35. 'ClustersX40'
  36. 'ClustersX50'
  37. 'Clusters_RNALabels'
In [7]:
#explain why each column is being dropped
#NEURONS
drop <- c("predictedCell_Co", "predictedGroup_RNA2ATACCo", "predictedScore_RNA2ATACCo", "predictedCell_Co_cell", 
         "predictedGroup_RNA2ATACCo_cell", "predictedScore_RNA2ATACCo_cell", "Neuron_Type")
Neur_vec <- names(getCellColData(projNeuron))
Neur_vec <- Neur_vec[Neur_vec %ni% drop]
df_Neuron = getCellColData(projNeuron, select = Neur_vec) #Neuron_type was manual annotations that aren't relevant anymore

#Set integrated labels as predictedXXXX_RNA2ATAC
colnames(df_Neuron)[which(names(df_Neuron) == "predictedCell_clustertype")] <- "predictedCell_RNA2ATAC"
colnames(df_Neuron)[which(names(df_Neuron) == "predictedGroup_RNA2ATAC_clustertype")] <- "predictedGroup_RNA2ATAC"
colnames(df_Neuron)[which(names(df_Neuron) == "predictedScore_RNA2ATAC_clustertype")] <- "predictedScore_RNA2ATAC"
names(df_Neuron)

#GLIA
drop = c("ClustersX10_tmp",'ClustersX10','ClustersX20','ClustersX30','ClustersX40','ClustersX50')
Glia_vec <- names(getCellColData(projGlia))
Glia_vec <- Glia_vec[Glia_vec %ni% drop]
Glia_vec #names of columns we want to keep
df_Glia = getCellColData(projGlia, select = Glia_vec)

#REPLACE predictedXXXX_RNA2ATAC WITH CLUSTERS_RNALABELS
df_Glia$predictedGroup_RNA2ATACCo = df_Glia$Clusters_RNALabels
df_Glia = df_Glia[,-31]
colnames(df_Glia)[which(names(df_Glia) == "predictedCell_Co")] <- "predictedCell_RNA2ATAC"
colnames(df_Glia)[which(names(df_Glia) == "predictedGroup_RNA2ATACCo")] <- "predictedGroup_RNA2ATAC"
colnames(df_Glia)[which(names(df_Glia) == "predictedScore_RNA2ATACCo")] <- "predictedScore_RNA2ATAC"
names(df_Glia)
table(df_Glia$Celltype1)
table(df_Glia$predictedGroup_RNA2ATAC)
  1. 'Sample'
  2. 'TSSEnrichment'
  3. 'ReadsInTSS'
  4. 'ReadsInPromoter'
  5. 'ReadsInBlacklist'
  6. 'PromoterRatio'
  7. 'PassQC'
  8. 'NucleosomeRatio'
  9. 'nMultiFrags'
  10. 'nMonoFrags'
  11. 'nFrags'
  12. 'nDiFrags'
  13. 'DoubletScore'
  14. 'DoubletEnrichment'
  15. 'BlacklistRatio'
  16. 'Sample_ID'
  17. 'Date.nuclei.prep'
  18. 'Biological.rep'
  19. 'Age'
  20. 'Sex'
  21. 'Species'
  22. 'Region'
  23. 'ClustersI200'
  24. 'ClustersH200'
  25. 'logNFrags'
  26. 'Celltype1'
  27. 'ClustersX60'
  28. 'ClustersX20'
  29. 'ClustersX10'
  30. 'predictedCell_RNA2ATAC'
  31. 'predictedGroup_RNA2ATAC'
  32. 'predictedScore_RNA2ATAC'
  1. 'Sample'
  2. 'TSSEnrichment'
  3. 'ReadsInTSS'
  4. 'ReadsInPromoter'
  5. 'ReadsInBlacklist'
  6. 'PromoterRatio'
  7. 'PassQC'
  8. 'NucleosomeRatio'
  9. 'nMultiFrags'
  10. 'nMonoFrags'
  11. 'nFrags'
  12. 'nDiFrags'
  13. 'DoubletScore'
  14. 'DoubletEnrichment'
  15. 'BlacklistRatio'
  16. 'Sample_ID'
  17. 'Date.nuclei.prep'
  18. 'Biological.rep'
  19. 'Age'
  20. 'Sex'
  21. 'Species'
  22. 'Region'
  23. 'ClustersI200'
  24. 'ClustersH200'
  25. 'logNFrags'
  26. 'Celltype1'
  27. 'ClustersX60'
  28. 'predictedCell_Co'
  29. 'predictedGroup_RNA2ATACCo'
  30. 'predictedScore_RNA2ATACCo'
  31. 'Clusters_RNALabels'
  1. 'Sample'
  2. 'TSSEnrichment'
  3. 'ReadsInTSS'
  4. 'ReadsInPromoter'
  5. 'ReadsInBlacklist'
  6. 'PromoterRatio'
  7. 'PassQC'
  8. 'NucleosomeRatio'
  9. 'nMultiFrags'
  10. 'nMonoFrags'
  11. 'nFrags'
  12. 'nDiFrags'
  13. 'DoubletScore'
  14. 'DoubletEnrichment'
  15. 'BlacklistRatio'
  16. 'Sample_ID'
  17. 'Date.nuclei.prep'
  18. 'Biological.rep'
  19. 'Age'
  20. 'Sex'
  21. 'Species'
  22. 'Region'
  23. 'ClustersI200'
  24. 'ClustersH200'
  25. 'logNFrags'
  26. 'Celltype1'
  27. 'ClustersX60'
  28. 'predictedCell_RNA2ATAC'
  29. 'predictedGroup_RNA2ATAC'
  30. 'predictedScore_RNA2ATAC'
Astrocyte  Meninges     Micro     Oligo       OPC   Schwann 
    13355       603      3284     33256       781      4085 
    Astrocyte.1     Astrocyte.2     Endothelial Ependymal.cells        Meninges 
           2417           10926             788             951               2 
      Microglia           Mural         Oligo.1         Oligo.2             OPC 
           2328             736           32624            1244            3348
In [9]:
Glia_columns = names(df_Glia)
Neuron_columns = names(df_Neuron)

Neuron_columns
Glia_columns
  1. 'Sample'
  2. 'TSSEnrichment'
  3. 'ReadsInTSS'
  4. 'ReadsInPromoter'
  5. 'ReadsInBlacklist'
  6. 'PromoterRatio'
  7. 'PassQC'
  8. 'NucleosomeRatio'
  9. 'nMultiFrags'
  10. 'nMonoFrags'
  11. 'nFrags'
  12. 'nDiFrags'
  13. 'DoubletScore'
  14. 'DoubletEnrichment'
  15. 'BlacklistRatio'
  16. 'Sample_ID'
  17. 'Date.nuclei.prep'
  18. 'Biological.rep'
  19. 'Age'
  20. 'Sex'
  21. 'Species'
  22. 'Region'
  23. 'ClustersI200'
  24. 'ClustersH200'
  25. 'logNFrags'
  26. 'Celltype1'
  27. 'ClustersX60'
  28. 'ClustersX20'
  29. 'ClustersX10'
  30. 'predictedCell_RNA2ATAC'
  31. 'predictedGroup_RNA2ATAC'
  32. 'predictedScore_RNA2ATAC'
  1. 'Sample'
  2. 'TSSEnrichment'
  3. 'ReadsInTSS'
  4. 'ReadsInPromoter'
  5. 'ReadsInBlacklist'
  6. 'PromoterRatio'
  7. 'PassQC'
  8. 'NucleosomeRatio'
  9. 'nMultiFrags'
  10. 'nMonoFrags'
  11. 'nFrags'
  12. 'nDiFrags'
  13. 'DoubletScore'
  14. 'DoubletEnrichment'
  15. 'BlacklistRatio'
  16. 'Sample_ID'
  17. 'Date.nuclei.prep'
  18. 'Biological.rep'
  19. 'Age'
  20. 'Sex'
  21. 'Species'
  22. 'Region'
  23. 'ClustersI200'
  24. 'ClustersH200'
  25. 'logNFrags'
  26. 'Celltype1'
  27. 'ClustersX60'
  28. 'predictedCell_RNA2ATAC'
  29. 'predictedGroup_RNA2ATAC'
  30. 'predictedScore_RNA2ATAC'
In [10]:
table(df_Neuron$predictedGroup_RNA2ATAC)
table(df_Glia$predictedGroup_RNA2ATAC)

  GABA1 GABA2_1 GABA2_2   GABA3 GABA4_1 GABA4_2   GABA5   GLUT1  GLUT10  GLUT11 
   1078      64    1545     376     967     795    1320    1092     431      39 
  GLUT2   GLUT3   GLUT4   GLUT5   GLUT6   GLUT7   GLUT8   GLUT9  midVen 
   2452    1945     341     992    2195    2283    1157       1    1518 
    Astrocyte.1     Astrocyte.2     Endothelial Ependymal.cells        Meninges 
           2417           10926             788             951               2 
      Microglia           Mural         Oligo.1         Oligo.2             OPC 
           2328             736           32624            1244            3348
In [11]:
#check to see if this merge is working properly
columns = names(df_Glia)
df_label = rbind(df_Neuron[,columns],df_Glia[,columns] )
df_label
dim(df_label)
print(getCellColData(proj))

DataFrame with 75955 rows and 30 columns
                                                  Sample TSSEnrichment
                                             <character>     <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse_DH_SEA2253A58        14.164
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse_DH_SEA2253A58        15.910
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse_DH_SEA2253A58        10.861
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse_DH_SEA2253A58        17.269
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC Mouse_DH_SEA2253A58        18.201
...                                                  ...           ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse_DH_SEA2253A69        10.693
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse_DH_SEA2253A69        17.317
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse_DH_SEA2253A69        11.675
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse_DH_SEA2253A69        13.119
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse_DH_SEA2253A69        30.716
                                     ReadsInTSS ReadsInPromoter
                                      <numeric>       <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA       6788           24952
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT       6990           25965
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG       4355           16936
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG       7718           27008
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC       7445           25859
...                                         ...             ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC        243            1056
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG        446            1576
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA        283            1280
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT        318            1255
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG        667            2131
                                     ReadsInBlacklist PromoterRatio    PassQC
                                            <numeric>     <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA             3777      0.155608         1
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT             3880      0.176551         1
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG             3561      0.115299         1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG             4147      0.185642         1
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC             5408      0.183335         1
...                                               ...           ...       ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC              138      0.156816         1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG              268      0.235505         1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA              208      0.194057         1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT              164      0.192780         1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG              170      0.332449         1
                                     NucleosomeRatio nMultiFrags nMonoFrags
                                           <numeric>   <numeric>  <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA        0.919877        6002      41761
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT        1.359279        8719      31168
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG        1.350735        7665      31243
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG        0.868773        4609      38925
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC        0.883453        5368      37444
...                                              ...         ...        ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC        9.203030         721        330
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG        1.428157         438       1378
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA        4.676420         681        581
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT        7.410853         707        387
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG        0.510368         150       2122
                                        nFrags  nDiFrags DoubletScore
                                     <numeric> <numeric>    <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA     80176     32413            0
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT     73534     33647            0
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG     73444     34536            0
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG     72742     29208            0
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC     70524     27712            0
...                                        ...       ...          ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC      3367      2316            0
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG      3346      1530            0
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA      3298      2036            0
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT      3255      2161            0
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG      3205       933            0
                                     DoubletEnrichment BlacklistRatio
                                             <numeric>      <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA         0.3000000      0.0235544
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT         0.0666667      0.0263824
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG         0.2666667      0.0242430
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG         0.4000000      0.0285049
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC         0.5666667      0.0383416
...                                                ...            ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC         0.2444444      0.0204930
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG         0.0222222      0.0400478
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA         0.0000000      0.0315343
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT         0.3555556      0.0251920
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG         0.6444444      0.0265211
                                       Sample_ID Date.nuclei.prep
                                     <character>      <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC  SEA2253A58       2022-02-15
...                                          ...              ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG  SEA2253A69       2022-02-23
                                     Biological.rep       Age         Sex
                                        <character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC     Mouse01-10  0.134247    F/M pool
...                                             ...       ...         ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG     Mouse11-20  0.156164    F/M pool
                                         Species      Region ClustersI200
                                     <character> <character>  <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC       Mouse  DorsalHorn           C9
...                                          ...         ...          ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC       Mouse  DorsalHorn          C24
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG       Mouse  DorsalHorn           C1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA       Mouse  DorsalHorn           C1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT       Mouse  DorsalHorn          C24
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG       Mouse  DorsalHorn          C24
                                     ClustersH200 logNFrags   Celltype1
                                      <character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA          C14   4.90404         EXC
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT          C11   4.86649         EXC
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG          C11   4.86596         EXC
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG          C11   4.86179         EXC
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC          C11   4.84834         EXC
...                                           ...       ...         ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC          C24   3.52724       Oligo
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG           C1   3.52453       Micro
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA           C1   3.51825       Micro
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT          C24   3.51255       Oligo
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG          C24   3.50583       Oligo
                                     ClustersX60 predictedCell_RNA2ATAC
                                     <character>            <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA          C6                    877
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT          C9                   2290
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG         C12                   1303
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG         C10                   8064
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC         C16                   4865
...                                          ...                    ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC         C16                   9822
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG         C20                   6548
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA         C20                  10602
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT         C16                   9822
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG         C19                   2160
                                     predictedGroup_RNA2ATAC
                                                 <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA                  midVen
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT                  midVen
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG                   GABA1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG                  midVen
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC                  midVen
...                                                      ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC                 Oligo.1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG               Microglia
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA               Microglia
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT                 Oligo.1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG                 Oligo.1
                                     predictedScore_RNA2ATAC
                                                   <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA                1.000000
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT                0.948107
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG                0.850651
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG                0.408128
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC                0.475185
...                                                      ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC                0.925414
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG                1.000000
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA                0.981841
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT                0.968747
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG                0.860995
  1. 75955
  2. 30
DataFrame with 75955 rows and 29 columns
                                                  Sample TSSEnrichment
                                             <character>     <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse_DH_SEA2253A58        14.164
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse_DH_SEA2253A58        15.910
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse_DH_SEA2253A58        10.861
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse_DH_SEA2253A58        17.269
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Mouse_DH_SEA2253A58        25.310
...                                                  ...           ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse_DH_SEA2253A69        10.693
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse_DH_SEA2253A69        17.317
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse_DH_SEA2253A69        11.675
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse_DH_SEA2253A69        13.119
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse_DH_SEA2253A69        30.716
                                     ReadsInTSS ReadsInPromoter
                                      <numeric>       <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA       6788           24952
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT       6990           25965
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG       4355           16936
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG       7718           27008
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC      13881           45719
...                                         ...             ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC        243            1056
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG        446            1576
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA        283            1280
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT        318            1255
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG        667            2131
                                     ReadsInBlacklist PromoterRatio    PassQC
                                            <numeric>     <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA             3777      0.155608         1
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT             3880      0.176551         1
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG             3561      0.115299         1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG             4147      0.185642         1
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC             3927      0.314804         1
...                                               ...           ...       ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC              138      0.156816         1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG              268      0.235505         1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA              208      0.194057         1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT              164      0.192780         1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG              170      0.332449         1
                                     NucleosomeRatio nMultiFrags nMonoFrags
                                           <numeric>   <numeric>  <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA        0.919877        6002      41761
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT        1.359279        8719      31168
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG        1.350735        7665      31243
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG        0.868773        4609      38925
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC        0.627884        6400      44607
...                                              ...         ...        ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC        9.203030         721        330
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG        1.428157         438       1378
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA        4.676420         681        581
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT        7.410853         707        387
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG        0.510368         150       2122
                                        nFrags  nDiFrags DoubletScore
                                     <numeric> <numeric>    <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA     80176     32413            0
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT     73534     33647            0
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG     73444     34536            0
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG     72742     29208            0
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC     72615     21608            0
...                                        ...       ...          ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC      3367      2316            0
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG      3346      1530            0
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA      3298      2036            0
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT      3255      2161            0
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG      3205       933            0
                                     DoubletEnrichment BlacklistRatio
                                             <numeric>      <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA         0.3000000      0.0235544
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT         0.0666667      0.0263824
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG         0.2666667      0.0242430
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG         0.4000000      0.0285049
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC         0.7666667      0.0270399
...                                                ...            ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC         0.2444444      0.0204930
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG         0.0222222      0.0400478
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA         0.0000000      0.0315343
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT         0.3555556      0.0251920
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG         0.6444444      0.0265211
                                       Sample_ID Date.nuclei.prep
                                     <character>      <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC  SEA2253A58       2022-02-15
...                                          ...              ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG  SEA2253A69       2022-02-23
                                     Biological.rep       Age         Sex
                                        <character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC     Mouse01-10  0.134247    F/M pool
...                                             ...       ...         ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG     Mouse11-20  0.156164    F/M pool
                                         Species      Region ClustersI200
                                     <character> <character>  <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC       Mouse  DorsalHorn          C20
...                                          ...         ...          ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC       Mouse  DorsalHorn          C24
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG       Mouse  DorsalHorn           C1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA       Mouse  DorsalHorn           C1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT       Mouse  DorsalHorn          C24
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG       Mouse  DorsalHorn          C24
                                     ClustersH200 logNFrags   Celltype1
                                      <character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA          C14   4.90404     midVent
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT          C11   4.86649     midVent
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG          C11   4.86596    Inh-Cdh3
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG          C11   4.86179     midVent
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC          C20   4.86103       Micro
...                                           ...       ...         ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC          C24   3.52724       Oligo
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG           C1   3.52453       Micro
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA           C1   3.51825       Micro
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT          C24   3.51255       Oligo
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG          C24   3.50583       Oligo
                                     predictedGroup_RNA2ATACCo ReadsInPeaks
                                                   <character>    <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA                    midVen        63912
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT                    midVen        67120
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG                     GABA1        52386
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG                    midVen        66616
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC           Ependymal.cells        98301
...                                                        ...          ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC                   Oligo.1         2783
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG                 Microglia         3402
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA                 Microglia         2753
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT                   Oligo.1         3079
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG                   Oligo.1         4068
                                          FRIP
                                     <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA  0.398623
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT  0.456443
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG  0.356678
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG  0.457930
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC  0.676930
...                                        ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC  0.413399
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG  0.508824
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA  0.417374
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT  0.472965
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG  0.634831
In [12]:
proj <- addCellColData(ArchRProj = proj, data = df_label$predictedGroup_RNA2ATAC,
    cells = rownames(df_label), name = "predictedGroup_RNA2ATAC", force = TRUE)
#proj <- addCellColData(ArchRProj = proj, data = df_label$Celltype1,
#    cells = rownames(df_label), name = "Celltype1", force = TRUE)
In [13]:
proj
getCellColData(proj)

           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    


class: ArchRProject 
outputDirectory: /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchRProjects/Mouse_DorsalHorn_scATAC 
samples(12): Mouse_DH_SEA2253A58 Mouse_DH_SEA2253A59 ...
  Mouse_DH_SEA2253A68 Mouse_DH_SEA2253A69
sampleColData names(8): ArrowFiles Sample_ID ... Species Region
cellColData names(30): Sample TSSEnrichment ... FRIP
  predictedGroup_RNA2ATAC
numberOfCells(1): 75955
medianTSS(1): 23.946
medianFrags(1): 16376
DataFrame with 75955 rows and 30 columns
                                                  Sample TSSEnrichment
                                             <character>     <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse_DH_SEA2253A58        14.164
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse_DH_SEA2253A58        15.910
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse_DH_SEA2253A58        10.861
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse_DH_SEA2253A58        17.269
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Mouse_DH_SEA2253A58        25.310
...                                                  ...           ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse_DH_SEA2253A69        10.693
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse_DH_SEA2253A69        17.317
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse_DH_SEA2253A69        11.675
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse_DH_SEA2253A69        13.119
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse_DH_SEA2253A69        30.716
                                     ReadsInTSS ReadsInPromoter
                                      <numeric>       <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA       6788           24952
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT       6990           25965
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG       4355           16936
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG       7718           27008
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC      13881           45719
...                                         ...             ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC        243            1056
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG        446            1576
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA        283            1280
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT        318            1255
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG        667            2131
                                     ReadsInBlacklist PromoterRatio    PassQC
                                            <numeric>     <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA             3777      0.155608         1
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT             3880      0.176551         1
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG             3561      0.115299         1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG             4147      0.185642         1
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC             3927      0.314804         1
...                                               ...           ...       ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC              138      0.156816         1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG              268      0.235505         1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA              208      0.194057         1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT              164      0.192780         1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG              170      0.332449         1
                                     NucleosomeRatio nMultiFrags nMonoFrags
                                           <numeric>   <numeric>  <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA        0.919877        6002      41761
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT        1.359279        8719      31168
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG        1.350735        7665      31243
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG        0.868773        4609      38925
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC        0.627884        6400      44607
...                                              ...         ...        ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC        9.203030         721        330
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG        1.428157         438       1378
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA        4.676420         681        581
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT        7.410853         707        387
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG        0.510368         150       2122
                                        nFrags  nDiFrags DoubletScore
                                     <numeric> <numeric>    <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA     80176     32413            0
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT     73534     33647            0
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG     73444     34536            0
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG     72742     29208            0
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC     72615     21608            0
...                                        ...       ...          ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC      3367      2316            0
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG      3346      1530            0
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA      3298      2036            0
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT      3255      2161            0
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG      3205       933            0
                                     DoubletEnrichment BlacklistRatio
                                             <numeric>      <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA         0.3000000      0.0235544
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT         0.0666667      0.0263824
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG         0.2666667      0.0242430
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG         0.4000000      0.0285049
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC         0.7666667      0.0270399
...                                                ...            ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC         0.2444444      0.0204930
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG         0.0222222      0.0400478
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA         0.0000000      0.0315343
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT         0.3555556      0.0251920
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG         0.6444444      0.0265211
                                       Sample_ID Date.nuclei.prep
                                     <character>      <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC  SEA2253A58       2022-02-15
...                                          ...              ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG  SEA2253A69       2022-02-23
                                     Biological.rep       Age         Sex
                                        <character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC     Mouse01-10  0.134247    F/M pool
...                                             ...       ...         ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG     Mouse11-20  0.156164    F/M pool
                                         Species      Region ClustersI200
                                     <character> <character>  <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC       Mouse  DorsalHorn          C20
...                                          ...         ...          ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC       Mouse  DorsalHorn          C24
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG       Mouse  DorsalHorn           C1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA       Mouse  DorsalHorn           C1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT       Mouse  DorsalHorn          C24
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG       Mouse  DorsalHorn          C24
                                     ClustersH200 logNFrags   Celltype1
                                      <character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA          C14   4.90404     midVent
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT          C11   4.86649     midVent
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG          C11   4.86596    Inh-Cdh3
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG          C11   4.86179     midVent
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC          C20   4.86103       Micro
...                                           ...       ...         ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC          C24   3.52724       Oligo
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG           C1   3.52453       Micro
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA           C1   3.51825       Micro
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT          C24   3.51255       Oligo
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG          C24   3.50583       Oligo
                                     predictedGroup_RNA2ATACCo ReadsInPeaks
                                                   <character>    <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA                    midVen        63912
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT                    midVen        67120
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG                     GABA1        52386
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG                    midVen        66616
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC           Ependymal.cells        98301
...                                                        ...          ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC                   Oligo.1         2783
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG                 Microglia         3402
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA                 Microglia         2753
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT                   Oligo.1         3079
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG                   Oligo.1         4068
                                          FRIP predictedGroup_RNA2ATAC
                                     <numeric>             <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA  0.398623                  midVen
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT  0.456443                  midVen
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG  0.356678                   GABA1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG  0.457930                  midVen
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC  0.676930         Ependymal.cells
...                                        ...                     ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC  0.413399                 Oligo.1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG  0.508824               Microglia
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA  0.417374               Microglia
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT  0.472965                 Oligo.1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG  0.634831                 Oligo.1
In [5]:
table(proj$Celltype1)
table(proj$predictedGroup_RNA2ATACCo)
table(proj$predictedGroup_RNA2ATAC)

  Astrocyte    Ex-Cpne4      Ex-Maf    Ex-Prkcg     Ex-Reln    Ex-Rreb1 
      13355        1330        2134         523        3426           5 
    Ex-Sox5 Inh-Adamts5    Inh-Cdh3     Inh-Npy    Inh-Pdyn    Inh-Rorb 
       5592        2296        1073         405        1308        1105 
   Meninges       Micro     midVent       Oligo         OPC     Schwann 
        603        3284        1394       33256         781        4085 
    Astrocyte.1     Astrocyte.2     Endothelial Ependymal.cells           GABA1 
           2417           10926             788             951            1077 
          GABA2           GABA3           GABA4           GABA5           GLUT1 
           1606             405            1786            1310             564 
         GLUT10          GLUT11           GLUT2           GLUT3           GLUT4 
            289               8            2848            1604             806 
          GLUT5           GLUT6           GLUT7           GLUT8           GLUT9 
              5            2892            2135            1586              56 
       Meninges       Microglia          midVen           Mural         Oligo.1 
              2            2328            1614             736           32624 
        Oligo.2             OPC 
           1244            3348 
    Astrocyte.1     Astrocyte.2     Endothelial Ependymal.cells           GABA1 
           2417           10926             788             951            1078 
        GABA2_1         GABA2_2           GABA3         GABA4_1         GABA4_2 
             64            1545             376             967             795 
          GABA5           GLUT1          GLUT10          GLUT11           GLUT2 
           1320            1092             431              39            2452 
          GLUT3           GLUT4           GLUT5           GLUT6           GLUT7 
           1945             341             992            2195            2283 
          GLUT8           GLUT9        Meninges       Microglia          midVen 
           1157               1               2            2328            1518 
          Mural         Oligo.1         Oligo.2             OPC 
            736           32624            1244            3348
In [20]:
## subset to cells with integrated labels
idxPass <- which(!is.na(proj$predictedGroup_RNA2ATACCo) & 
                 proj$predictedGroup_RNA2ATACCo %ni% c('Drop', 'NA.', 'TH')) # too few cluster

#impute weights dropped, 'cell-x-cell' matrix
cellsPass <- proj$cellNames[idxPass]
proj = subsetCells(ArchRProj = proj, cellNames = cellsPass)
proj
getCellColData(proj)

           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
    


class: ArchRProject 
outputDirectory: /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchRProjects/Mouse_DorsalHorn_scATAC 
samples(12): Mouse_DH_SEA2253A58 Mouse_DH_SEA2253A59 ...
  Mouse_DH_SEA2253A68 Mouse_DH_SEA2253A69
sampleColData names(8): ArrowFiles Sample_ID ... Species Region
cellColData names(29): Sample TSSEnrichment ... ReadsInPeaks FRIP
numberOfCells(1): 75955
medianTSS(1): 23.946
medianFrags(1): 16376
DataFrame with 75955 rows and 29 columns
                                                  Sample TSSEnrichment
                                             <character>     <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse_DH_SEA2253A58        14.164
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse_DH_SEA2253A58        15.910
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse_DH_SEA2253A58        10.861
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse_DH_SEA2253A58        17.269
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Mouse_DH_SEA2253A58        25.310
...                                                  ...           ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse_DH_SEA2253A69        10.693
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse_DH_SEA2253A69        17.317
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse_DH_SEA2253A69        11.675
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse_DH_SEA2253A69        13.119
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse_DH_SEA2253A69        30.716
                                     ReadsInTSS ReadsInPromoter
                                      <numeric>       <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA       6788           24952
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT       6990           25965
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG       4355           16936
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG       7718           27008
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC      13881           45719
...                                         ...             ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC        243            1056
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG        446            1576
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA        283            1280
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT        318            1255
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG        667            2131
                                     ReadsInBlacklist PromoterRatio    PassQC
                                            <numeric>     <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA             3777      0.155608         1
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT             3880      0.176551         1
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG             3561      0.115299         1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG             4147      0.185642         1
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC             3927      0.314804         1
...                                               ...           ...       ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC              138      0.156816         1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG              268      0.235505         1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA              208      0.194057         1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT              164      0.192780         1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG              170      0.332449         1
                                     NucleosomeRatio nMultiFrags nMonoFrags
                                           <numeric>   <numeric>  <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA        0.919877        6002      41761
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT        1.359279        8719      31168
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG        1.350735        7665      31243
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG        0.868773        4609      38925
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC        0.627884        6400      44607
...                                              ...         ...        ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC        9.203030         721        330
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG        1.428157         438       1378
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA        4.676420         681        581
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT        7.410853         707        387
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG        0.510368         150       2122
                                        nFrags  nDiFrags DoubletScore
                                     <numeric> <numeric>    <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA     80176     32413            0
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT     73534     33647            0
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG     73444     34536            0
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG     72742     29208            0
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC     72615     21608            0
...                                        ...       ...          ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC      3367      2316            0
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG      3346      1530            0
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA      3298      2036            0
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT      3255      2161            0
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG      3205       933            0
                                     DoubletEnrichment BlacklistRatio
                                             <numeric>      <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA         0.3000000      0.0235544
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT         0.0666667      0.0263824
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG         0.2666667      0.0242430
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG         0.4000000      0.0285049
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC         0.7666667      0.0270399
...                                                ...            ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC         0.2444444      0.0204930
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG         0.0222222      0.0400478
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA         0.0000000      0.0315343
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT         0.3555556      0.0251920
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG         0.6444444      0.0265211
                                       Sample_ID Date.nuclei.prep
                                     <character>      <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC  SEA2253A58       2022-02-15
...                                          ...              ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG  SEA2253A69       2022-02-23
                                     Biological.rep       Age         Sex
                                        <character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC     Mouse01-10  0.134247    F/M pool
...                                             ...       ...         ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG     Mouse11-20  0.156164    F/M pool
                                         Species      Region ClustersI200
                                     <character> <character>  <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC       Mouse  DorsalHorn          C20
...                                          ...         ...          ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC       Mouse  DorsalHorn          C24
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG       Mouse  DorsalHorn           C1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA       Mouse  DorsalHorn           C1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT       Mouse  DorsalHorn          C24
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG       Mouse  DorsalHorn          C24
                                     ClustersH200 logNFrags       Celltype1
                                      <character> <numeric>     <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA          C14   4.90404         midVent
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT          C11   4.86649         midVent
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG          C11   4.86596        Inh-Cdh3
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG          C11   4.86179         midVent
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC          C20   4.86103 Ependymal.cells
...                                           ...       ...             ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC          C24   3.52724         Oligo.1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG           C1   3.52453       Microglia
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA           C1   3.51825       Microglia
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT          C24   3.51255         Oligo.1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG          C24   3.50583         Oligo.1
                                     predictedGroup_RNA2ATACCo ReadsInPeaks
                                                   <character>    <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA                    midVen        63912
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT                    midVen        67120
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG                     GABA1        52386
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG                    midVen        66616
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC           Ependymal.cells        98301
...                                                        ...          ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC                   Oligo.1         2783
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG                 Microglia         3402
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA                 Microglia         2753
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT                   Oligo.1         3079
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG                   Oligo.1         4068
                                          FRIP
                                     <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA  0.398623
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT  0.456443
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG  0.356678
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG  0.457930
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC  0.676930
...                                        ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC  0.413399
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG  0.508824
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA  0.417374
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT  0.472965
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG  0.634831
In [15]:
## make UMAP plots
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData", 
                    name = "Sample", embedding = "UMAPH200")

p2 <- plotEmbedding(proj, colorBy = "cellColData", 
                    name = "Celltype1", embedding = "UMAPH200")

p3 <- plotEmbedding(proj, colorBy = "cellColData", 
                    name = "predictedGroup_RNA2ATACCo", embedding = "UMAPH200")

p4 <- plotEmbedding(proj, colorBy = "cellColData", 
                    name = "predictedGroup_RNA2ATAC", embedding = "UMAPH200")


ggAlignPlots(p1, p2, p3, p4,  type = "h")

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-6a69f3940f522-Date-2023-01-31_Time-21-54-23.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = cellColData

Plotting Embedding

1 
WARNING: Error found with Cairo installation. Continuing without rasterization.



ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-6a69f3940f522-Date-2023-01-31_Time-21-54-23.log

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-6a69f7a2bb031-Date-2023-01-31_Time-21-54-42.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = cellColData

Plotting Embedding

1 
WARNING: Error found with Cairo installation. Continuing without rasterization.



ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-6a69f7a2bb031-Date-2023-01-31_Time-21-54-42.log

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-6a69f66db3091-Date-2023-01-31_Time-21-54-45.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = cellColData

Plotting Embedding

1 
WARNING: Error found with Cairo installation. Continuing without rasterization.

Length of unique values greater than palette, interpolating..



ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-6a69f66db3091-Date-2023-01-31_Time-21-54-45.log

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-6a69f2faf7889-Date-2023-01-31_Time-21-54-48.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = cellColData

Plotting Embedding

1 
WARNING: Error found with Cairo installation. Continuing without rasterization.

Length of unique values greater than palette, interpolating..



ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-6a69f2faf7889-Date-2023-01-31_Time-21-54-48.log
In [22]:
proj <- addImputeWeights(proj, reducedDims = "HarmonyI200")

ArchR logging to : ArchRLogs/ArchR-addImputeWeights-5b3435d52c362-Date-2023-01-30_Time-10-51-35.log
If there is an issue, please report to github with logFile!

2023-01-30 10:51:38 : Computing Impute Weights Using Magic (Cell 2018), 0 mins elapsed.
In [19]:
## Neuron vs. Glia markers
markerGenes1  <- c('SRRM3',#Neurons
                   'MYT1L',#Neurons
                   'RBFOX3'#Neurons
                  )

p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix", 
                    name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
  x + guides(color = FALSE, fill = FALSE) + 
    theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
    theme(  axis.text.x=element_blank(),  axis.ticks.x=element_blank(), 
            axis.text.y=element_blank(),  axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))

Getting ImputeWeights

No imputeWeights found, returning NULL

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e6bcd96e4-Date-2022-10-21_Time-10-08-59.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = GeneScoreMatrix

Getting Matrix Values...

2022-10-21 10:09:01 : 



Plotting Embedding

1 
2 
3 


ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e6bcd96e4-Date-2022-10-21_Time-10-08-59.log

Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [18]:
## Neuron vs. Glia markers
markerGenes1  <- c('ITGB4',#Astrocyte1
                   'GFAP',#Astrocyte1
                   'SLC7A10',#Astrocyte2
                   'PDZRN4'#Astrocyte2
                  )

p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix", 
                    name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
  x + guides(color = FALSE, fill = FALSE) + 
    theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
    theme(  axis.text.x=element_blank(),  axis.ticks.x=element_blank(), 
            axis.text.y=element_blank(),  axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))

Getting ImputeWeights

No imputeWeights found, returning NULL

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-5b3434dab729e-Date-2023-01-30_Time-10-38-51.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = GeneScoreMatrix

Getting Matrix Values...

2023-01-30 10:39:43 : 



Plotting Embedding

1 
2 
3 
4 


ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-5b3434dab729e-Date-2023-01-30_Time-10-38-51.log

Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [36]:
## Neuron vs. Glia markers
markerGenes1  <- c('RFX2'#Ependymal 
#                    'DNAH12'#Ependymal 
                  )

p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix", 
                    name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
  x + guides(color = FALSE, fill = FALSE) + 
    theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
    theme(  axis.text.x=element_blank(),  axis.ticks.x=element_blank(), 
            axis.text.y=element_blank(),  axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))

Getting ImputeWeights

No imputeWeights found, returning NULL

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e227ae1be-Date-2022-10-21_Time-10-22-57.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = GeneScoreMatrix

Getting Matrix Values...

2022-10-21 10:22:58 : 



Plotting Embedding

1 


ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e227ae1be-Date-2022-10-21_Time-10-22-57.log

Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”

Error in x + guides(color = FALSE, fill = FALSE): non-numeric argument to binary operator
Traceback:

1. lapply(p, function(x) {
 .     x + guides(color = FALSE, fill = FALSE) + theme_ArchR(baseSize = 6.5) + 
 .         theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) + theme(axis.text.x = element_blank(), 
 .         axis.ticks.x = element_blank(), axis.text.y = element_blank(), 
 .         axis.ticks.y = element_blank())
 . })
2. lapply(p, function(x) {
 .     x + guides(color = FALSE, fill = FALSE) + theme_ArchR(baseSize = 6.5) + 
 .         theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) + theme(axis.text.x = element_blank(), 
 .         axis.ticks.x = element_blank(), axis.text.y = element_blank(), 
 .         axis.ticks.y = element_blank())
 . })
3. FUN(X[[i]], ...)
In [19]:
## Neuron vs. Glia markers
markerGenes1  <- c('LAMA2',#Meninges
                   'BICC1'#Meninges
                  )

p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix", 
                    name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
  x + guides(color = FALSE, fill = FALSE) + 
    theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
    theme(  axis.text.x=element_blank(),  axis.ticks.x=element_blank(), 
            axis.text.y=element_blank(),  axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))

Getting ImputeWeights

No imputeWeights found, returning NULL

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-5b34352a6a59c-Date-2023-01-30_Time-10-40-56.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = GeneScoreMatrix

Getting Matrix Values...

2023-01-30 10:41:19 : 



Plotting Embedding

1 
2 


ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-5b34352a6a59c-Date-2023-01-30_Time-10-40-56.log

Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [4]:
## Neuron vs. Glia markers
markerGenes1  <- c('Flt1',#Endothelial
                   'Notch3'#Mural
                  )

p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix", 
                    name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
  x + guides(color = FALSE, fill = FALSE) + 
    theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
    theme(  axis.text.x=element_blank(),  axis.ticks.x=element_blank(), 
            axis.text.y=element_blank(),  axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))

Getting ImputeWeights

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-41a44169b6b4-Date-2023-02-15_Time-10-12-05.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = GeneIntegrationMatrix

Getting Matrix Values...

2023-02-15 10:12:13 : 

Warning message in mclapply(..., mc.cores = threads, mc.preschedule = preschedule):
“12 function calls resulted in an error”

Error in .safelapply(seq_along(cellNamesList), function(x) {: 
Error Found Iteration 1 : 
	[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList,  : \n  Exiting See Error Above\n"
	<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>
Error Found Iteration 2 : 
	[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList,  : \n  Exiting See Error Above\n"
	<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>
Error Found Iteration 3 : 
	[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList,  : \n  Exiting See Error Above\n"
	<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>
Error Found Iteration 4 : 
	[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList,  : \n  Exiting See Error Above\n"
	<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>
Error Found Iteration 5 : 
	[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList,  : \n  Exiting See Error Above\n"
	<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>
Error Found Iteration 6 : 
	[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList,  : \n  Exiting See Error Above\n"
	<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>
Error Found Iteration 7 : 
	[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList,  : \n  Exiting See Error Above\n"
	<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>
Error Found Iteration 8 : 
	[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList,  : \n  Exiting See Error Above\n"
	<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>
Error Found Iteration 9 : 
	[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList,  : \n  Exiting See Error Above\n"
	<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>
Error Found Iteration 10 : 
	[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList,  : \n  Exiting See Error Above\n"
	<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>
Error Found Iteration 11 : 
	[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList,  : \n  Exiting See Error Above\n"
	<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>
Error Found Iteration 12 : 
	[1] "Error in .logError(e, fn = \".getMatFromArrow\", info = \"\", errorList = errorList,  : \n  Exiting See Error Above\n"
	<simpleError in .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList,     logFile = logFile): Exiting See Error Above>

Traceback:

1. plotEmbedding(ArchRProj = proj, colorBy = "GeneIntegrationMatrix", 
 .     name = markerGenes1, embedding = "UMAPH200")
2. .getMatrixValues(ArchRProj = ArchRProj, name = name, matrixName = colorBy, 
 .     log2Norm = FALSE, threads = threads, logFile = logFile)
3. .safelapply(seq_along(cellNamesList), function(x) {
 .     if (getArchRVerbose()) 
 .         message(x, " ", appendLF = FALSE)
 .     valuesx <- tryCatch({
 .         o <- h5closeAll()
 .         ArrowFile <- getSampleColData(ArchRProj)[names(cellNamesList)[x], 
 .             "ArrowFiles"]
 .         valuesx <- .getMatFromArrow(ArrowFile = ArrowFile, featureDF = featureDF, 
 .             binarize = FALSE, useMatrix = matrixName, cellNames = cellNamesList[[x]], 
 .             threads = 1)
 .         colnames(valuesx) <- cellNamesList[[x]]
 .         valuesx
 .     }, error = function(e) {
 .         errorList <- list(x = x, ArrowFile = ArrowFile, ArchRProj = ArchRProj, 
 .             cellNames = ArchRProj$cellNames, cellNamesList = cellNamesList, 
 .             featureDF = featureDF)
 .         .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList, 
 .             logFile = logFile)
 .     })
 .     valuesx
 . }, threads = threads) %>% Reduce("cbind", .)
4. Reduce("cbind", .)
5. .safelapply(seq_along(cellNamesList), function(x) {
 .     if (getArchRVerbose()) 
 .         message(x, " ", appendLF = FALSE)
 .     valuesx <- tryCatch({
 .         o <- h5closeAll()
 .         ArrowFile <- getSampleColData(ArchRProj)[names(cellNamesList)[x], 
 .             "ArrowFiles"]
 .         valuesx <- .getMatFromArrow(ArrowFile = ArrowFile, featureDF = featureDF, 
 .             binarize = FALSE, useMatrix = matrixName, cellNames = cellNamesList[[x]], 
 .             threads = 1)
 .         colnames(valuesx) <- cellNamesList[[x]]
 .         valuesx
 .     }, error = function(e) {
 .         errorList <- list(x = x, ArrowFile = ArrowFile, ArchRProj = ArchRProj, 
 .             cellNames = ArchRProj$cellNames, cellNamesList = cellNamesList, 
 .             featureDF = featureDF)
 .         .logError(e, fn = ".getMatFromArrow", info = "", errorList = errorList, 
 .             logFile = logFile)
 .     })
 .     valuesx
 . }, threads = threads)
6. stop(errorMsg)
In [34]:
## Neuron vs. Glia markers
markerGenes1  <- c('MYO1F',#Microglia
                   'PALD1' #Microglia
                  )

p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix", 
                    name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
  x + guides(color = FALSE, fill = FALSE) + 
    theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
    theme(  axis.text.x=element_blank(),  axis.ticks.x=element_blank(), 
            axis.text.y=element_blank(),  axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))

Getting ImputeWeights

No imputeWeights found, returning NULL

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e28130342-Date-2022-10-21_Time-10-22-07.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = GeneScoreMatrix

Getting Matrix Values...

2022-10-21 10:22:10 : 



Plotting Embedding

1 
2 


ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e28130342-Date-2022-10-21_Time-10-22-07.log

Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [33]:
## Neuron vs. Glia markers
markerGenes1  <- c('QDPR',#Oligo1
                   'DPY19L1'#Oligo2
                  )

p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix", 
                    name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
  x + guides(color = FALSE, fill = FALSE) + 
    theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
    theme(  axis.text.x=element_blank(),  axis.ticks.x=element_blank(), 
            axis.text.y=element_blank(),  axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))

Getting ImputeWeights

No imputeWeights found, returning NULL

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7ede42222-Date-2022-10-21_Time-10-21-37.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = GeneScoreMatrix

Getting Matrix Values...

2022-10-21 10:21:38 : 



Plotting Embedding

1 
2 


ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7ede42222-Date-2022-10-21_Time-10-21-37.log

Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [32]:
## Neuron vs. Glia markers
markerGenes1  <- c('MEGF11',#OPC
                   'TNR'#OPC
                  )

p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix", 
                    name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
  x + guides(color = FALSE, fill = FALSE) + 
    theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
    theme(  axis.text.x=element_blank(),  axis.ticks.x=element_blank(), 
            axis.text.y=element_blank(),  axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))

Getting ImputeWeights

No imputeWeights found, returning NULL

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e374b11be-Date-2022-10-21_Time-10-21-08.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = GeneScoreMatrix

Getting Matrix Values...

2022-10-21 10:21:11 : 



Plotting Embedding

1 
2 


ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e374b11be-Date-2022-10-21_Time-10-21-08.log

Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [25]:
## Neuron vs. Glia markers
markerGenes1  <- c('MPZ',#Schwann
                   'PMP22'#Schwann
                  )

p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix", 
                    name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
  x + guides(color = FALSE, fill = FALSE) + 
    theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
    theme(  axis.text.x=element_blank(),  axis.ticks.x=element_blank(), 
            axis.text.y=element_blank(),  axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))

Getting ImputeWeights

No imputeWeights found, returning NULL

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e2195493-Date-2022-10-21_Time-10-13-35.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = GeneScoreMatrix

Getting Matrix Values...

2022-10-21 10:13:38 : 



Plotting Embedding

1 
2 


ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e2195493-Date-2022-10-21_Time-10-13-35.log

Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [26]:
## Excitatory vs. Inhibitory markers
markerGenes1  <- c('SLC17A6','FSTL4', # Excitatory 
                   'SLC32A1','PAX2' # Inhibitory
                  )

p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix", 
                    name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
  x + guides(color = FALSE, fill = FALSE) + 
    theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
    theme(  axis.text.x=element_blank(),  axis.ticks.x=element_blank(), 
            axis.text.y=element_blank(),  axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))

Getting ImputeWeights

No imputeWeights found, returning NULL

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e918fa13-Date-2022-10-21_Time-10-14-07.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = GeneScoreMatrix

Getting Matrix Values...

2022-10-21 10:14:10 : 



Plotting Embedding

1 
2 
3 
4 


ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e918fa13-Date-2022-10-21_Time-10-14-07.log

Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [27]:
## Marker Genes for differentiation of Excitatory Neurons
markerGenes1  <- c('GFRA1',
                   'CRHR2',
                   'COL13A1',
                   'NMUR2',
#                    'TAC3',
                   'NMU',
                   'COL5A2',
                   'GHR',
                   'COL24A1',
                   'NMBR',
                   'TAC1',
#                    'ANOS1',
                   'FSTL4',
                   'ADARB2',
                   'MAF',
                   'ST8SIA6',
                   'MAFA',
                   'NTNG1',
                   'ADAMTS16',
                   'TLL2',
                   'OTOGL'
                  )

p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix", 
                    name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
  x + guides(color = FALSE, fill = FALSE) + 
    theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
    theme(  axis.text.x=element_blank(),  axis.ticks.x=element_blank(), 
            axis.text.y=element_blank(),  axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))

Getting ImputeWeights

No imputeWeights found, returning NULL

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e7efe2284-Date-2022-10-21_Time-10-15-05.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = GeneScoreMatrix

Getting Matrix Values...

2022-10-21 10:15:08 : 



Plotting Embedding

1 
2 
3 
4 
5 
6 
7 
8 
9 
10 
11 
12 
13 
14 
15 
16 
17 
18 
19 


ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e7efe2284-Date-2022-10-21_Time-10-15-05.log

Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [28]:
## Marker Genes for differentiation of Inhibitory Nuerons
markerGenes1  <- c('MASP1',
                   'RREB1',
                   'NPY',
                   'MET',
                   'PTN',
                   'PDYN'
                  )

p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix", 
                    name = markerGenes1, embedding = "UMAPH200")
p <- lapply(p, function(x){
  x + guides(color = FALSE, fill = FALSE) + 
    theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
    theme(  axis.text.x=element_blank(),  axis.ticks.x=element_blank(), 
            axis.text.y=element_blank(),  axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))

Getting ImputeWeights

No imputeWeights found, returning NULL

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e4c3c03a7-Date-2022-10-21_Time-10-17-19.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = GeneScoreMatrix

Getting Matrix Values...

2022-10-21 10:17:20 : 



Plotting Embedding

1 
2 
3 
4 
5 
6 


ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e4c3c03a7-Date-2022-10-21_Time-10-17-19.log

Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
Warning message:
“`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
In [29]:
## make UMAP plots of
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData", 
                    name = "ClustersH200", embedding = "UMAPH200")

p2 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData", 
                    name = "DoubletEnrichment", embedding = "UMAPH200")

ggAlignPlots(p1, p2, type = "h")

proj$logNFrags = log10(proj$nFrags)

p3 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData", 
                    name = "logNFrags", embedding = "UMAPH200")

ggAlignPlots(p1, p3, type = "h")

p4 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData", 
                    name = "TSSEnrichment", embedding = "UMAPH200")

ggAlignPlots(p1, p4, type = "h")

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e842a4ec-Date-2022-10-21_Time-10-18-11.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = cellColData

Plotting Embedding

1 
WARNING: Error found with Cairo installation. Continuing without rasterization.



ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e842a4ec-Date-2022-10-21_Time-10-18-11.log

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e51d6d3b8-Date-2022-10-21_Time-10-18-12.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = cellColData

Plotting Embedding

1 


ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e51d6d3b8-Date-2022-10-21_Time-10-18-12.log

ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7ef066510-Date-2022-10-21_Time-10-18-19.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = cellColData

Plotting Embedding

1 


ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7ef066510-Date-2022-10-21_Time-10-18-19.log


ArchR logging to : ArchRLogs/ArchR-plotEmbedding-44b7e27ef7ad6-Date-2022-10-21_Time-10-18-26.log
If there is an issue, please report to github with logFile!

Getting UMAP Embedding

ColorBy = cellColData

Plotting Embedding

1 


ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-44b7e27ef7ad6-Date-2022-10-21_Time-10-18-26.log
In [16]:
proj = saveArchRProject(proj)

Saving ArchRProject...

Loading ArchRProject...

Successfully loaded ArchRProject!


                                                   / |
                                                 /    \
            .                                  /      |.
            \\\                              /        |.
              \\\                          /           `|.
                \\\                      /              |.
                  \                    /                |\
                  \\#####\           /                  ||
                ==###########>      /                   ||
                 \\##==......\    /                     ||
            ______ =       =|__ /__                     ||      \\\
        ,--' ,----`-,__ ___/'  --,-`-===================##========>
       \               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
        -,____,---'       \\####\\________________,--\\_##,/
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
In [6]:
library(BSgenome.Mmusculus.UCSC.mm10)

Loading required package: BSgenome

Loading required package: Biostrings

Loading required package: XVector


Attaching package: ‘XVector’


The following object is masked from ‘package:purrr’:

    compact


The following object is masked from ‘package:plyr’:

    compact



Attaching package: ‘Biostrings’


The following object is masked from ‘package:grid’:

    pattern


The following object is masked from ‘package:base’:

    strsplit


Loading required package: rtracklayer

Call peaks using integrated clusters¶

In [8]:
# make group coverage, call peaks, and 
proj<-addGroupCoverages(proj, groupBy="predictedGroup_RNA2ATAC", 
                        minReplicates = 5, maxReplicates = 11, force = TRUE,
                        minCells = 40, maxCells = 1000)

ArchR logging to : ArchRLogs/ArchR-addGroupCoverages-2d9e2ec554f6-Date-2023-02-01_Time-21-48-53.log
If there is an issue, please report to github with logFile!

Astrocyte.1 (1 of 29) : CellGroups N = 11

Astrocyte.2 (2 of 29) : CellGroups N = 11

Endothelial (3 of 29) : CellGroups N = 11

Ependymal.cells (4 of 29) : CellGroups N = 11

GABA1 (5 of 29) : CellGroups N = 11

GABA2_1 (6 of 29) : CellGroups N = 5

GABA2_2 (7 of 29) : CellGroups N = 11

GABA3 (8 of 29) : CellGroups N = 5

GABA4_1 (9 of 29) : CellGroups N = 11

GABA4_2 (10 of 29) : CellGroups N = 11

GABA5 (11 of 29) : CellGroups N = 11

GLUT1 (12 of 29) : CellGroups N = 11

GLUT2 (13 of 29) : CellGroups N = 11

GLUT3 (14 of 29) : CellGroups N = 11

GLUT4 (15 of 29) : CellGroups N = 5

GLUT5 (16 of 29) : CellGroups N = 11

GLUT6 (17 of 29) : CellGroups N = 11

GLUT7 (18 of 29) : CellGroups N = 11

GLUT8 (19 of 29) : CellGroups N = 11

GLUT9 (20 of 29) : CellGroups N = 5

GLUT10 (21 of 29) : CellGroups N = 6

GLUT11 (22 of 29) : CellGroups N = 5

Meninges (23 of 29) : CellGroups N = 5

Microglia (24 of 29) : CellGroups N = 11

midVen (25 of 29) : CellGroups N = 11

Mural (26 of 29) : CellGroups N = 11

Oligo.1 (27 of 29) : CellGroups N = 11

Oligo.2 (28 of 29) : CellGroups N = 11

OPC (29 of 29) : CellGroups N = 11

2023-02-01 21:50:18 : Creating Coverage Files!, 1.419 mins elapsed.

2023-02-01 21:50:18 : Batch Execution w/ safelapply!, 1.419 mins elapsed.

2023-02-01 23:11:56 : Adding Kmer Bias to Coverage Files!, 83.04 mins elapsed.

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2023-02-01 23:47:41 : Finished Creation of Coverage Files!, 118.801 mins elapsed.

ArchR logging successful to : ArchRLogs/ArchR-addGroupCoverages-2d9e2ec554f6-Date-2023-02-01_Time-21-48-53.log
In [10]:
proj = saveArchRProject(proj)

Saving ArchRProject...

Loading ArchRProject...

Successfully loaded ArchRProject!


                                                   / |
                                                 /    \
            .                                  /      |.
            \\\                              /        |.
              \\\                          /           `|.
                \\\                      /              |.
                  \                    /                |\
                  \\#####\           /                  ||
                ==###########>      /                   ||
                 \\##==......\    /                     ||
            ______ =       =|__ /__                     ||      \\\
        ,--' ,----`-,__ ___/'  --,-`-===================##========>
       \               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
        -,____,---'       \\####\\________________,--\\_##,/
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
In [9]:
# call peaks 
proj<-addReproduciblePeakSet(proj, groupBy = "predictedGroup_RNA2ATAC", reproducibility = "(n + 1)/2",
                             plot = FALSE, genomeSize = 2.7e9)

Searching For MACS2..

Found with $path!

ArchR logging to : ArchRLogs/ArchR-addReproduciblePeakSet-2d9e276e9063-Date-2023-02-01_Time-23-47-42.log
If there is an issue, please report to github with logFile!

Calling Peaks with Macs2

2023-02-01 23:47:44 : Peak Calling Parameters!, 0.027 mins elapsed.


                          Group nCells nCellsUsed nReplicates nMin nMax
Astrocyte.1         Astrocyte.1   2417       2295          11  122  293
Astrocyte.2         Astrocyte.2  10926       9492          11  677 1000
Endothelial         Endothelial    788        736          11   57   85
Ependymal.cells Ependymal.cells    951        903          11   56  113
GABA1                     GABA1   1078       1015          11   64  120
GABA2_1                 GABA2_1     64         63           5   40   40
GABA2_2                 GABA2_2   1545       1453          11  102  155
GABA3                     GABA3    376        376           5   43   97
GABA4_1                 GABA4_1    967        916          11   61  107
GABA4_2                 GABA4_2    795        749          11   48   94
GABA5                     GABA5   1320       1248          11   78  151
GLUT1                     GLUT1   1092       1032          11   70  131
GLUT2                     GLUT2   2452       2297          11  156  279
GLUT3                     GLUT3   1945       1826          11  127  216
GLUT4                     GLUT4    341        341           5   65   69
GLUT5                     GLUT5    992        928          11   64  109
GLUT6                     GLUT6   2195       2058          11  147  236
GLUT7                     GLUT7   2283       2153          11  139  244
GLUT8                     GLUT8   1157       1082          11   78  120
GLUT9                     GLUT9      1          1           5    1    1
GLUT10                   GLUT10    431        431           6   42  209
GLUT11                   GLUT11     39         39           5   21   27
Meninges               Meninges      2          2           5    2    2
Microglia             Microglia   2328       2185          11  152  244
midVen                   midVen   1518       1430          11   98  166
Mural                     Mural    736        693          11   45   81
Oligo.1                 Oligo.1  32624      11000          11 1000 1000
Oligo.2                 Oligo.2   1244       1175          11   73  139
OPC                         OPC   3348       3168          11  202  369
                maxPeaks
Astrocyte.1       150000
Astrocyte.2       150000
Endothelial       150000
Ependymal.cells   150000
GABA1             150000
GABA2_1            31500
GABA2_2           150000
GABA3             150000
GABA4_1           150000
GABA4_2           150000
GABA5             150000
GLUT1             150000
GLUT2             150000
GLUT3             150000
GLUT4             150000
GLUT5             150000
GLUT6             150000
GLUT7             150000
GLUT8             150000
GLUT9                500
GLUT10            150000
GLUT11             19500
Meninges            1000
Microglia         150000
midVen            150000
Mural             150000
Oligo.1           150000
Oligo.2           150000
OPC               150000

2023-02-01 23:47:44 : Batching Peak Calls!, 0.028 mins elapsed.

2023-02-01 23:47:46 : Batch Execution w/ safelapply!, 0 mins elapsed.

2023-02-02 01:28:26 : Identifying Reproducible Peaks!, 100.729 mins elapsed.

2023-02-02 01:30:36 : Creating Union Peak Set!, 102.887 mins elapsed.

Converged after 9 iterations!

2023-02-02 01:30:54 : Finished Creating Union Peak Set (518748)!, 103.194 mins elapsed.
In [10]:
# add peak counts matrix 
proj <- addPeakMatrix(proj)

ArchR logging to : ArchRLogs/ArchR-addPeakMatrix-1c87954e054fd-Date-2023-02-09_Time-12-36-27.log
If there is an issue, please report to github with logFile!

2023-02-09 12:36:28 : Batch Execution w/ safelapply!, 0 mins elapsed.

Overriding previous entry for ReadsInPeaks

Overriding previous entry for FRIP

ArchR logging successful to : ArchRLogs/ArchR-addPeakMatrix-1c87954e054fd-Date-2023-02-09_Time-12-36-27.log
In [11]:
BiocManager::install("JASPAR2020")
library(JASPAR2020)

'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cran.r-project.org


Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.3 (2022-03-10)

Installing package(s) 'JASPAR2020'

Updating HTML index of packages in '.Library'

Making 'packages.html' ...
 done

Old packages: 'brew', 'clue', 'commonmark', 'cpp11', 'curl', 'data.table',
  'desc', 'devtools', 'digest', 'evaluate', 'gargle', 'gert', 'gh', 'gitcreds',
  'haven', 'isoband', 'lifecycle', 'nlme', 'openssl', 'pracma', 'ragg',
  'RCurl', 'readr', 'rmarkdown', 'RSQLite', 'sys', 'testthat', 'tidyselect',
  'tinytex', 'vroom', 'xfun', 'XML', 'yaml', 'zip'
In [7]:
# add motif enrichment matrix
proj <- addMotifAnnotations(ArchRProj = proj, motifSet = "encode", name = "Motif",logFile = createLogFile("addMotifAnnotations"), species = getGenome(proj), force = TRUE)

ArchR logging to : ArchRLogs/ArchR-addMotifAnnotations-1c879242927da-Date-2023-02-09_Time-11-47-15.log
If there is an issue, please report to github with logFile!

peakAnnotation name already exists! Overriding.

2023-02-09 11:47:15 : Gettting Motif Set, Species : BSgenome.Mmusculus.UCSC.mm10, 0.004 mins elapsed.

2023-02-09 11:47:23 : Finding Motif Positions with motifmatchr!, 0.142 mins elapsed.

2023-02-09 12:32:55 : All Motifs Overlap at least 1 peak!, 45.668 mins elapsed.

2023-02-09 12:32:55 : Creating Motif Overlap Matrix, 45.668 mins elapsed.

2023-02-09 12:33:12 : Finished Getting Motif Info!, 45.957 mins elapsed.

ArchR logging successful to : ArchRLogs/ArchR-addMotifAnnotations-1c879242927da-Date-2023-02-09_Time-11-47-15.log
In [11]:
# # add motif deviations matrix
proj <- addBgdPeaks(proj, force =  TRUE)

Identifying Background Peaks!
In [5]:
#not run
proj <- addDeviationsMatrix(proj,  peakAnnotation = "Motif", force = TRUE)

Identifying Background Peaks!

ArchR logging to : ArchRLogs/ArchR-addDeviationsMatrix-206be1585f45d-Date-2023-02-10_Time-09-45-41.log
If there is an issue, please report to github with logFile!


NULL

as(<lgCMatrix>, "dgCMatrix") is deprecated since Matrix 1.5-0; do as(., "dMatrix") instead

2023-02-10 09:46:06 : Batch Execution w/ safelapply!, 0 mins elapsed.

###########
2023-02-10 20:57:46 : Completed Computing Deviations!, 672.082 mins elapsed.
###########

ArchR logging successful to : ArchRLogs/ArchR-addDeviationsMatrix-206be1585f45d-Date-2023-02-10_Time-09-45-41.log
In [6]:
proj = saveArchRProject(proj)

Saving ArchRProject...

Loading ArchRProject...

Successfully loaded ArchRProject!


                                                   / |
                                                 /    \
            .                                  /      |.
            \\\                              /        |.
              \\\                          /           `|.
                \\\                      /              |.
                  \                    /                |\
                  \\#####\           /                  ||
                ==###########>      /                   ||
                 \\##==......\    /                     ||
            ______ =       =|__ /__                     ||      \\\
        ,--' ,----`-,__ ___/'  --,-`-===================##========>
       \               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
        -,____,---'       \\####\\________________,--\\_##,/
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
In [9]:
plotVarDev <- getVarDeviations(proj, name = "MotifMatrix")
  1. 'GeneIntegrationMatrix'
  2. 'GeneScoreMatrix'
  3. 'MotifMatrix'
  4. 'PeakMatrix'
  5. 'TileMatrix'
In [13]:
# add co-accessibility matrix
proj <- addCoAccessibility(proj, reducedDims = "HarmonyI200", dimsToUse = 1:30,
                           scaleDims = TRUE, corCutOff = 0.75, k = 100, 
                           knnIteration = 500, overlapCutoff = 0.8, 
                           maxDist = 1e+05, scaleTo = 10^4, log2Norm = TRUE)

ArchR logging to : ArchRLogs/ArchR-addCoAccessibility-44b7e20e09826-Date-2022-10-21_Time-09-13-02.log
If there is an issue, please report to github with logFile!

2022-10-21 09:13:02 : Computing KNN, 0.003 mins elapsed.

2022-10-21 09:13:03 : Identifying Non-Overlapping KNN pairs, 0.011 mins elapsed.

2022-10-21 09:13:07 : Identified 498 Groupings!, 0.076 mins elapsed.

2022-10-21 09:14:08 : Computing Co-Accessibility chr1 (1 of 20), 1.102 mins elapsed.

2022-10-21 09:14:54 : Computing Co-Accessibility chr2 (2 of 20), 1.87 mins elapsed.

2022-10-21 09:15:52 : Computing Co-Accessibility chr3 (3 of 20), 2.833 mins elapsed.

2022-10-21 09:16:35 : Computing Co-Accessibility chr4 (4 of 20), 3.557 mins elapsed.

2022-10-21 09:17:27 : Computing Co-Accessibility chr5 (5 of 20), 4.413 mins elapsed.

2022-10-21 09:18:18 : Computing Co-Accessibility chr6 (6 of 20), 5.275 mins elapsed.

2022-10-21 09:19:01 : Computing Co-Accessibility chr7 (7 of 20), 5.987 mins elapsed.

2022-10-21 09:19:52 : Computing Co-Accessibility chr8 (8 of 20), 6.828 mins elapsed.

2022-10-21 09:20:30 : Computing Co-Accessibility chr9 (9 of 20), 7.467 mins elapsed.

2022-10-21 09:21:18 : Computing Co-Accessibility chr10 (10 of 20), 8.26 mins elapsed.

2022-10-21 09:22:01 : Computing Co-Accessibility chr11 (11 of 20), 8.977 mins elapsed.

2022-10-21 09:23:01 : Computing Co-Accessibility chr12 (12 of 20), 9.984 mins elapsed.

2022-10-21 09:23:40 : Computing Co-Accessibility chr13 (13 of 20), 10.635 mins elapsed.

2022-10-21 09:24:19 : Computing Co-Accessibility chr14 (14 of 20), 11.277 mins elapsed.

2022-10-21 09:24:53 : Computing Co-Accessibility chr15 (15 of 20), 11.848 mins elapsed.

2022-10-21 09:25:27 : Computing Co-Accessibility chr16 (16 of 20), 12.417 mins elapsed.

2022-10-21 09:26:00 : Computing Co-Accessibility chr17 (17 of 20), 12.961 mins elapsed.

2022-10-21 09:26:38 : Computing Co-Accessibility chr18 (18 of 20), 13.598 mins elapsed.

2022-10-21 09:27:10 : Computing Co-Accessibility chr19 (19 of 20), 14.134 mins elapsed.

2022-10-21 09:27:40 : Computing Co-Accessibility chrX (20 of 20), 14.635 mins elapsed.

ArchR logging successful to : ArchRLogs/ArchR-addCoAccessibility-44b7e20e09826-Date-2022-10-21_Time-09-13-02.log
In [17]:
markerGenes  <- c('ITGB4',#Astrocyte1
                   'GFAP',#Astrocyte1
                   'SLC7A10',#Astrocyte2
                   'PDZRN4'#Astrocyte2
                  )

p <- plotBrowserTrack(
    ArchRProj = proj, 
    groupBy = "ClustersH200", 
    geneSymbol = markerGenes, 
    upstream = 50000,
    downstream = 50000,
    loops = getCoAccessibility(proj)
)

ArchR logging to : ArchRLogs/ArchR-plotBrowserTrack-44b7e797f5dd7-Date-2022-10-21_Time-10-04-51.log
If there is an issue, please report to github with logFile!

2022-10-21 10:04:51 : Validating Region, 0.009 mins elapsed.


GRanges object with 4 ranges and 2 metadata columns:
      seqnames              ranges strand |     gene_id      symbol
         <Rle>           <IRanges>  <Rle> | <character> <character>
  [1]    chr11 115974725-116008411      + |      192897       Itgb4
  [2]    chr11 102887336-102897200      - |       14580        Gfap
  [3]     chr7   35186385-35201111      + |       53896     Slc7a10
  [4]    chr15   92396810-92771819      + |      239618      Pdzrn4
  -------
  seqinfo: 21 sequences from mm10 genome

2022-10-21 10:04:51 : Adding Bulk Tracks (1 of 4), 0.011 mins elapsed.

2022-10-21 10:05:17 : Adding Feature Tracks (1 of 4), 0.437 mins elapsed.

2022-10-21 10:05:17 : Adding Loop Tracks (1 of 4), 0.438 mins elapsed.

2022-10-21 10:05:21 : Adding Gene Tracks (1 of 4), 0.507 mins elapsed.

2022-10-21 10:05:21 : Plotting, 0.51 mins elapsed.

2022-10-21 10:05:25 : Adding Bulk Tracks (2 of 4), 0.574 mins elapsed.

2022-10-21 10:05:45 : Adding Feature Tracks (2 of 4), 0.899 mins elapsed.

2022-10-21 10:05:45 : Adding Loop Tracks (2 of 4), 0.9 mins elapsed.

2022-10-21 10:05:49 : Adding Gene Tracks (2 of 4), 0.969 mins elapsed.

2022-10-21 10:05:50 : Plotting, 0.989 mins elapsed.

2022-10-21 10:05:54 : Adding Bulk Tracks (3 of 4), 1.053 mins elapsed.

2022-10-21 10:06:13 : Adding Feature Tracks (3 of 4), 1.379 mins elapsed.

2022-10-21 10:06:13 : Adding Loop Tracks (3 of 4), 1.38 mins elapsed.

2022-10-21 10:06:23 : Adding Gene Tracks (3 of 4), 1.543 mins elapsed.

2022-10-21 10:06:23 : Plotting, 1.547 mins elapsed.

2022-10-21 10:06:28 : Adding Bulk Tracks (4 of 4), 1.625 mins elapsed.

2022-10-21 10:06:46 : Adding Feature Tracks (4 of 4), 1.93 mins elapsed.

2022-10-21 10:06:46 : Adding Loop Tracks (4 of 4), 1.93 mins elapsed.

2022-10-21 10:06:48 : Adding Gene Tracks (4 of 4), 1.956 mins elapsed.

2022-10-21 10:06:48 : Plotting, 1.959 mins elapsed.

ArchR logging successful to : ArchRLogs/ArchR-plotBrowserTrack-44b7e797f5dd7-Date-2022-10-21_Time-10-04-51.log
In [11]:
names(attributes(proj)$reducedDims)
  1. 'IterativeLSI30'
  2. 'IterativeLSI200'
  3. 'HarmonyI200'
In [8]:
proj = saveArchRProject(ArchRProj = proj)

Saving ArchRProject...

Loading ArchRProject...

Successfully loaded ArchRProject!


                                                   / |
                                                 /    \
            .                                  /      |.
            \\\                              /        |.
              \\\                          /           `|.
                \\\                      /              |.
                  \                    /                |\
                  \\#####\           /                  ||
                ==###########>      /                   ||
                 \\##==......\    /                     ||
            ______ =       =|__ /__                     ||      \\\
        ,--' ,----`-,__ ___/'  --,-`-===================##========>
       \               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
        -,____,---'       \\####\\________________,--\\_##,/
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|
In [5]:
getAvailableMatrices(proj)
  1. 'GeneIntegrationMatrix'
  2. 'GeneScoreMatrix'
  3. 'MotifMatrix'
  4. 'PeakMatrix'
  5. 'TileMatrix'
In [6]:
proj <- addCellColData(ArchRProj = proj, data = proj$predictedGroup_RNA2ATAC,
    cells = rownames(getCellColData(proj)), name = "FINAL_GROUP_LABEL", force = TRUE)
names(getCellColData(proj))
getCellColData(proj)
  1. 'Sample'
  2. 'TSSEnrichment'
  3. 'ReadsInTSS'
  4. 'ReadsInPromoter'
  5. 'ReadsInBlacklist'
  6. 'PromoterRatio'
  7. 'PassQC'
  8. 'NucleosomeRatio'
  9. 'nMultiFrags'
  10. 'nMonoFrags'
  11. 'nFrags'
  12. 'nDiFrags'
  13. 'DoubletScore'
  14. 'DoubletEnrichment'
  15. 'BlacklistRatio'
  16. 'Sample_ID'
  17. 'Date.nuclei.prep'
  18. 'Biological.rep'
  19. 'Age'
  20. 'Sex'
  21. 'Species'
  22. 'Region'
  23. 'ClustersI200'
  24. 'ClustersH200'
  25. 'logNFrags'
  26. 'Celltype1'
  27. 'predictedGroup_RNA2ATACCo'
  28. 'ReadsInPeaks'
  29. 'FRIP'
  30. 'predictedGroup_RNA2ATAC'
  31. 'FINAL_GROUP_LABEL'
DataFrame with 75955 rows and 31 columns
                                                  Sample TSSEnrichment
                                             <character>     <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse_DH_SEA2253A58        14.164
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse_DH_SEA2253A58        15.910
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse_DH_SEA2253A58        10.861
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse_DH_SEA2253A58        17.269
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC Mouse_DH_SEA2253A58        25.310
...                                                  ...           ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC Mouse_DH_SEA2253A69        10.693
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG Mouse_DH_SEA2253A69        17.317
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA Mouse_DH_SEA2253A69        11.675
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT Mouse_DH_SEA2253A69        13.119
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG Mouse_DH_SEA2253A69        30.716
                                     ReadsInTSS ReadsInPromoter
                                      <numeric>       <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA       6788           24952
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT       6990           25965
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG       4355           16936
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG       7718           27008
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC      13881           45719
...                                         ...             ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC        243            1056
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG        446            1576
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA        283            1280
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT        318            1255
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG        667            2131
                                     ReadsInBlacklist PromoterRatio    PassQC
                                            <numeric>     <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA             3777      0.155608         1
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT             3880      0.176551         1
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG             3561      0.115299         1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG             4147      0.185642         1
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC             3927      0.314804         1
...                                               ...           ...       ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC              138      0.156816         1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG              268      0.235505         1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA              208      0.194057         1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT              164      0.192780         1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG              170      0.332449         1
                                     NucleosomeRatio nMultiFrags nMonoFrags
                                           <numeric>   <numeric>  <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA        0.919877        6002      41761
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT        1.359279        8719      31168
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG        1.350735        7665      31243
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG        0.868773        4609      38925
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC        0.627884        6400      44607
...                                              ...         ...        ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC        9.203030         721        330
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG        1.428157         438       1378
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA        4.676420         681        581
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT        7.410853         707        387
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG        0.510368         150       2122
                                        nFrags  nDiFrags DoubletScore
                                     <numeric> <numeric>    <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA     80176     32413            0
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT     73534     33647            0
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG     73444     34536            0
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG     72742     29208            0
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC     72615     21608            0
...                                        ...       ...          ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC      3367      2316            0
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG      3346      1530            0
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA      3298      2036            0
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT      3255      2161            0
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG      3205       933            0
                                     DoubletEnrichment BlacklistRatio
                                             <numeric>      <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA         0.3000000      0.0235544
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT         0.0666667      0.0263824
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG         0.2666667      0.0242430
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG         0.4000000      0.0285049
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC         0.7666667      0.0270399
...                                                ...            ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC         0.2444444      0.0204930
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG         0.0222222      0.0400478
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA         0.0000000      0.0315343
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT         0.3555556      0.0251920
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG         0.6444444      0.0265211
                                       Sample_ID Date.nuclei.prep
                                     <character>      <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG  SEA2253A58       2022-02-15
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC  SEA2253A58       2022-02-15
...                                          ...              ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT  SEA2253A69       2022-02-23
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG  SEA2253A69       2022-02-23
                                     Biological.rep       Age         Sex
                                        <character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG     Mouse01-10  0.134247    F/M pool
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC     Mouse01-10  0.134247    F/M pool
...                                             ...       ...         ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT     Mouse11-20  0.156164    F/M pool
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG     Mouse11-20  0.156164    F/M pool
                                         Species      Region ClustersI200
                                     <character> <character>  <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG       Mouse  DorsalHorn          C11
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC       Mouse  DorsalHorn          C20
...                                          ...         ...          ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC       Mouse  DorsalHorn          C24
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG       Mouse  DorsalHorn           C1
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA       Mouse  DorsalHorn           C1
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT       Mouse  DorsalHorn          C24
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG       Mouse  DorsalHorn          C24
                                     ClustersH200 logNFrags   Celltype1
                                      <character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA          C14   4.90404     midVent
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT          C11   4.86649     midVent
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG          C11   4.86596    Inh-Cdh3
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG          C11   4.86179     midVent
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC          C20   4.86103       Micro
...                                           ...       ...         ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC          C24   3.52724       Oligo
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG           C1   3.52453       Micro
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA           C1   3.51825       Micro
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT          C24   3.51255       Oligo
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG          C24   3.50583       Oligo
                                     predictedGroup_RNA2ATACCo ReadsInPeaks
                                                   <character>    <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA                    midVen        63912
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT                    midVen        67120
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG                     GABA1        52386
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG                    midVen        66616
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC           Ependymal.cells        98301
...                                                        ...          ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC                   Oligo.1         2783
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG                 Microglia         3402
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA                 Microglia         2753
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT                   Oligo.1         3079
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG                   Oligo.1         4068
                                          FRIP predictedGroup_RNA2ATAC
                                     <numeric>             <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA  0.398623                  midVen
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT  0.456443                  midVen
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG  0.356678                   GABA1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG  0.457930                  midVen
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC  0.676930         Ependymal.cells
...                                        ...                     ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC  0.413399                 Oligo.1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG  0.508824               Microglia
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA  0.417374               Microglia
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT  0.472965                 Oligo.1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG  0.634831                 Oligo.1
                                     FINAL_GROUP_LABEL
                                           <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA            midVen
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT            midVen
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG             GABA1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG            midVen
Mouse_DH_SEA2253A58#GAGGGATACCTGGCAC   Ependymal.cells
...                                                ...
Mouse_DH_SEA2253A69#GACTACCCTGGCCATC           Oligo.1
Mouse_DH_SEA2253A69#GACAAGGTGCTGAGAG         Microglia
Mouse_DH_SEA2253A69#GACCTATGAGGTGCAA         Microglia
Mouse_DH_SEA2253A69#GACTACCCTTCGGGCT           Oligo.1
Mouse_DH_SEA2253A69#TAAAAAAAAAAAAAAG           Oligo.1
In [7]:
table(proj$predictedGroup_RNA2ATAC)
table(proj$FINAL_GROUP_LABEL)
proj = saveArchRProject(ArchRProj = proj)

    Astrocyte.1     Astrocyte.2     Endothelial Ependymal.cells           GABA1 
           2417           10926             788             951            1078 
        GABA2_1         GABA2_2           GABA3         GABA4_1         GABA4_2 
             64            1545             376             967             795 
          GABA5           GLUT1          GLUT10          GLUT11           GLUT2 
           1320            1092             431              39            2452 
          GLUT3           GLUT4           GLUT5           GLUT6           GLUT7 
           1945             341             992            2195            2283 
          GLUT8           GLUT9        Meninges       Microglia          midVen 
           1157               1               2            2328            1518 
          Mural         Oligo.1         Oligo.2             OPC 
            736           32624            1244            3348 
    Astrocyte.1     Astrocyte.2     Endothelial Ependymal.cells           GABA1 
           2417           10926             788             951            1078 
        GABA2_1         GABA2_2           GABA3         GABA4_1         GABA4_2 
             64            1545             376             967             795 
          GABA5           GLUT1          GLUT10          GLUT11           GLUT2 
           1320            1092             431              39            2452 
          GLUT3           GLUT4           GLUT5           GLUT6           GLUT7 
           1945             341             992            2195            2283 
          GLUT8           GLUT9        Meninges       Microglia          midVen 
           1157               1               2            2328            1518 
          Mural         Oligo.1         Oligo.2             OPC 
            736           32624            1244            3348 
Saving ArchRProject...

Loading ArchRProject...

Successfully loaded ArchRProject!


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                ==###########>      /                   ||
                 \\##==......\    /                     ||
            ______ =       =|__ /__                     ||      \\\
        ,--' ,----`-,__ ___/'  --,-`-===================##========>
       \               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
        -,____,---'       \\####\\________________,--\\_##,/
           ___      .______        ______  __    __  .______      
          /   \     |   _  \      /      ||  |  |  | |   _  \     
         /  ^  \    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\  \   |      /     |  |     |   __   | |      /     
       /  _____  \  |  |\  \\___ |  `----.|  |  |  | |  |\  \\___.
      /__/     \__\ | _| `._____| \______||__|  |__| | _| `._____|